The invention relates to materials and methods for detecting nucleic acid target sequences.
Sequence-specific hybridization of labeled oligonucleotide probes has long been used as a means for detecting and identifying selected nucleotide sequences, and labeling of such probes with fluorescent labels has provided a relatively sensitive, nonradioactive means for facilitating detection of probe hybridization. Recently developed detection methods employ the process of fluorescence energy transfer (FET) rather than direct detection of fluorescence intensity for detection of probe hybridization. Fluorescence energy transfer occurs between a donor fluorophore and a quencher dye (which may or may not be a fluorophore) when the absorption spectrum of one (the quencher) overlaps the emission spectrum of the other (the donor) and the two dyes are in close proximity. Dyes with these properties are referred to as donor/quencher dye pairs or energy transfer dye pairs. The excited-state energy of the donor fluorophore is transferred by a resonance dipole-induced dipole interaction to the neighboring quencher. This results in quenching of donor fluorescence. In some cases, if the quencher is also a fluorophore, the intensity of its fluorescence may be enhanced. The efficiency of energy transfer is highly dependent on the distance between the donor and quencher, and equations predicting these relationships have been developed by Fxc3x6rster (1948. Ann. Phys. 2, 55-75). The distance between donor and quencher dyes at which energy transfer efficiency is 50% is referred to as the Fxc3x6rster distance (RO). Other mechanisms of fluorescence quenching are also known including, for example, charge transfer and collisional quenching.
Energy transfer and other mechanisms which rely on the interaction of two dyes in close proximity to produce quenching are an attractive means for detecting or identifying nucleotide sequences, as such assays may be conducted in homogeneous formats. Homogeneous assay formats are simpler than conventional probe hybridization assays which rely on detection of the fluorescence of a single fluorophore label, as heterogeneous assays generally require additional steps to separate hybridized label from free label. Typically, FET and related methods have relied upon monitoring a change in the fluorescence properties of one or both dye labels when they are brought together by the hybridization of two complementary oligonucleotides. In this format, the change in fluorescence properties may be measured as a change in the amount of energy transfer or as a change in the amount of fluorescence quenching, typically indicated as an increase in the fluorescence intensity of one of the dyes. In this way, the nucleotide sequence of interest may be detected without separation of unhybridized and hybridized oligonucleotides. The hybridization may occur between two separate complementary oligonucleotides, one of which is labeled with the donor fluorophore and one of which is labeled with the quencher. In double-stranded form there is decreased donor fluorescence (increased quenching) and/or increased energy transfer as compared to the single-stranded oligonucleotides. Several formats for FET hybridization assays are reviewed in Nonisotopic DNA Probe Techniques (1992. Academic Press, Inc., pgs. 311-352). Alternatively, the donor and quencher may be linked to a single oligonucleotide such that there is a detectable difference in the fluorescence properties of one or both when the oligonucleotide is unhybridized vs. when it is hybridized to its complementary sequence. In this format, donor fluorescence is typically increased and energy transfer/quenching are decreased when the oligonucleotide is hybridized. For example, a self-complementary oligonucleotide labeled at each end may form a hairpin which brings the two fluorophores (i.e., the 5xe2x80x2 and 3xe2x80x2 ends) into close spatial proximity where energy transfer and quenching can occur. Hybridization of the self-complementary oligonucleotide to its complementary sequence in a second oligonucleotide disrupts the hairpin and increases the distance between the two dyes, thus reducing quenching. A disadvantage of the hairpin structure is that it is very stable and conversion to the unquenched, hybridized form is often slow and only moderately favored, resulting in generally poor performance. Tyagi and Kramer (1996. Nature Biotech. 14, 303-308) describe a hairpin labeled as described above which comprises a detector sequence in the loop between the self-complementary arms of the hairpin which form the stem. The base-paired stem must melt in order for the detector sequence to hybridize to the target and cause a reduction in quenching. A xe2x80x9cdouble hairpinxe2x80x9d probe and methods of using it are described by B. Bagwell, et al. (1994. Nucl. Acids Res. 22, 2424-2425; U.S. Pat. No. 5,607,834). These structures contain the target binding sequence within the hairpin and therefore involve competitive hybridization between the target and the self-complementary sequences of the hairpin. Bagwell solves the problem of unfavorable hybridization kinetics by destabilizing the hairpin with mismatches.
Homogeneous methods employing energy transfer or other mechanisms of fluorescence quenching for detection of nucleic acid amplification have also been described. L. G. Lee, et al. (1993. Nuc. Acids Res. 21, 3761-3766) disclose a real-time detection method in which a doubly-labeled detector probe is cleaved in a target amplification-specific manner during PCR. The detector probe is hybridized downstream of the amplification primer so that the 5xe2x80x2-3xe2x80x2 exonuclease activity of Taq polymerase digests the detector probe, separating two fluorescent dyes which form an energy transfer pair. Fluorescence intensity increases as the probe is cleaved.
Signal primers (sometimes also referred to as detector probes) which hybridize to the target sequence downstream of the hybridization site of the amplification primers have been described for homogeneous detection of nucleic acid amplification (U.S. Pat. No. 5,547,861 which is incorporated herein by reference). The signal primer is extended by the polymerase in a manner similar to extension of the amplification primers. Extension of the amplification primer displaces the extension product of the signal primer in a target amplification-dependent manner, producing a double-stranded secondary amplification product which may be detected as an indication of target amplification. Examples of homogeneous detection methods for use with single-stranded signal primers are described in U.S. Pat. No. 5,550,025 (incorporation of lipophilic dyes and restriction sites) and U.S. Pat. No. 5,593,867 (fluorescence polarization detection). More recently signal primers have been adapted for detection of nucleic acid targets using FET methods. U.S. Pat. No. 5,691,145 discloses G-quartet structures containing donor/quencher dye pairs appended 5xe2x80x2 to the target binding sequence of a single-stranded signal primer. Synthesis of the complementary strand during target amplification unfolds the G-quartet, increasing the distance between the donor and quencher dye and resulting in a detectable incease in donor fluorescence. Partially single-stranded, partially double-stranded signal primers labeled with donor/quencher dye pairs have also recently been described. For example, EP 0 878 554 discloses signal primers with donor/quencher dye pairs flanking a single-stranded restriction endonuclease recognition site. In the presence of the target, the restriction site becomes double-stranded and cleavable by the restriction endonuclease. Cleavage separates the dye pair and decreases donor quenching. EP 0 881 302 describes signal primers with an intramolecularly base-paired structure appended thereto. The donor dye of a donor/quencher dye pair linked to the intramolecularly base-paired structure is quenched when the structure is folded, but in the presence of target a sequence complementary to the intramolecularly base-paired structure is synthesized. This unfolds the intramolecularly base-paired structure and separates the donor and quencher dyes, resulting in a decrease in donor quenching. Nazarenko, et al. (U.S. Pat. No. 5,866,336) describe a similar method where in amplification primers are configured with hairpin structures which carry donor/quencher dye pairs.
Energy transfer and other fluorescence quenching detection methods have also been applied to detecting a target sequence by hybridization of a specific probe. Japanese Patent No. 93015439 B discloses methods for measuring polynucleotides by hybridizing the single-stranded target to a single-stranded polynucleotide probe tagged with two labels which form an energy transfer pair. The double-stranded hybrid is cleaved between the labels by a-restriction enzyme and fluorescence of one of the labels is measured. A disadvantage of this method is that the restriction site in the probe must also be present in the target sequence being detected. S. S. Ghosh, et al. (1994. Nucl. Acids Res. 22, 3155-3159) describe restriction enzyme catalyzed cleavage of fluorophore-labeled oligonucleotides which are analyzed using fluorescence resonance energy transfer. In these assays, the complementary oligonucleotides are hybridized to produce the double-stranded restriction site, with one of the fluorescent labels linked to each of the two strands.
The present invention employs a signal primer for detection of nucleic acid target sequences. The signal primer comprises two oligonucleotides and is partially single-stranded and partially double-stranded. The first oligonucleotide is referred to as the adapter oligonucleotide. The adapter oligonucleotide is hybridized to a complementary second oligonucleotide such that the 3xe2x80x2 end of the adapter oligonucleotide forms a single-stranded tail region which hybridizes to the target sequence. The portion of the single-stranded 3xe2x80x2 tail which hybridizes to the target sequence is referred to as the target binding sequence. The region of the adapter oligonucleotide which is 5xe2x80x2 to the target binding sequence and the 3xe2x80x2 single-stranded tail hybridizes to the second oligonucleotide to form an intermolecularly base-paired, partially double-stranded signal primer molecule under the selected reaction conditions for hybridization of the signal primer to the target. The sequence of the adapter oligonucleotide to which the second oligonucleotide hybridizes (the 5xe2x80x2 adapter sequence) comprises a sequence which does not hybridize to the target. The 5xe2x80x2 adapter sequence may be selected such that it is the same in a variety of adapter oligonucleotides with different target binding sequences (i.e., a xe2x80x9cuniversalxe2x80x9d 5xe2x80x2 adapter sequence). This simplifies detection of a variety of different targets, as described below.
The signal primers of the present invention therefore have the advantage that a single labeled reporter probe (described below) may be used for detection of a variety of different target sequences, because a common 5xe2x80x2 adapter sequence for hybridiation to a second oligonucleotide may be appended to different target binding sequences in the adapter oligonucleotide. This simplifies synthesis of reporter probes and reduces the cost involved. Although the adapter oligonucleotides must have varying target binding sequences for recognition of different targets, they are easier and less costly to synthesize than reporter probes because they do not require labeling for use in the present invention.